The interaction of a molecular recognition element (MRE) or receptor with a surface-bound ligand varies substantially depending on how the ligand is presented. One important consideration in the presentation of a ligand to a receptor is the polarity of the ligand. In other words, a polymer/ligand will interact with a receptor differently in many instances when one "end" of the polymer is presented than when the opposite end is presented by the substrate. Such differential interaction is well known in the art for antibodies and corresponding antigens as well as enzymes and corresponding enzyme substrates (see Walsh, Enzymatic Reaction Mechanisms, W. H. Freeman and Co., New York, 1979, incorporated herein by reference for all purposes, for various examples of this differential interaction for enzymes and enzyme substrates).
Many molecules of biological interest, such as peptides, oligonucleotides, and carbohydrates, have an inherent polarity. For example peptides have an inherent polarity at their N and C termini, while oligonuleotides have inherent polarity in their 3' and 5' termini. Oligosaccharides also have an inherent polarity, having at least one hydroxyl group at one "end" and an anomeric center, with substantially different chemical reactivity at the other. The choice of which "end" of the polymer is to be tethered to a substrate during synthesis is generally governed by the chemistry required to build the polymer using solid-phase synthesis techniques. Peptides, for example, are frequently anchored to a substrate via their carboxyl terminus and the chemical synthesis proceeds on the terminal amino group (termed C to N or "Merrifield" synthesis) whereas nucleotides frequently have their 3' end anchored and the synthesis proceeds on the 5' end. Oligosaccharide solid-phase synthesis likewise proceeds with one end anchored and the other end available for reaction during synthesis.
Use of surface-bound ligands as a screening tool has necessitated the development of novel chemistries to provide for the presentation of polymers with both complementary polarities. For instance, proteins are typically sequenced from the amino terminus, but newer methods, see U.S. Pat. No. 5,064,767, incorporated herein by reference, provide for sequencing from the carboxyl terminus. Some have proposed that the polymers be fully synthesized and then attached to a solid support with reversed polarity. This is often a labor-intensive and inefficient process. In the case of peptides, one may alternatively simply reverse the direction of synthesis of the polymer so as to anchor the molecule via the terminal amino group and proceed with the synthesis on the carboxyl terminus (termed "N to C synthesis").
There are several reasons why conventional polymer synthesis techniques cannot be easily adapted to the synthesis of polymers having their "opposite" terminus exposed, where exposed refers to the end of the polymer not attached to the solid support. In the case of peptides, for example, one problem, although not fully understood, is believed to be racemization of the growing peptide chain in a reversed polymer synthesis scheme. Racemization has been proposed to occur via intramolecular attack of the amide oxygen of the adjacent residue on the activated ester of the terminal residue, leading to an intermediate oxazolinone prone to racemization. While prevention of racemization may be possible, it may be a difficult, costly, or complex problem to solve. This problem may be particularly difficult to solve in the case of synthesis of polymers of substantial length. For example, in a 10-step synthesis there will often be 9 possible racemization events producing up to 2.sup.9 =512 diastereomers.
In the case of nucleotide synthesis other problems are also not fully understood, but are believed to present difficulties. For example, there may be difficulty in selectively protecting the two types of hydroxyl groups (secondary versus primary) and the relative stabilities of the resultant compounds.
From the above it is seen that improved means and methods of synthesizing and presenting polymers on surfaces are desired.